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DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.

Bloodstream infections and invasive nontyphoidal Salmonellosis in particular remain a major health and economic burden worldwide. The complexity of blood matrixes along with extremely low concentration of pathogens in blood poses a great challenge for rapid and ultrasensitive detection. Sample preparation has been the critical step that should provide blood-matrix-free sample with the targeted pathogen in the highest possible concentration. In this work, we addressed this challenge by combining magnetic-bead-based pathogen concentration and solid-phase PCR (SP-PCR). The SP-PCR performed on a supercritical angle fluorescence (SAF) microlens array embedded in a microchip enabled quick and accurate detection of low levels of Salmonella enterica serovar typhimurium and enteritidis in blood samples without culture enrichment. Protein AG-magnetic beads immobilized with antisalmonella antibody could efficiently concentrate both Salmonella serovars with a capturing efficiency >95%. Higher tolerance of Phusion hot start DNA polymerase to PCR inhibitors and its compatibility with protein AG-magnetic beads allowed the integration of SP-PCR. Analysis of Salmonella-spiked blood samples with the SP-PCR resulted in a limit of detection (LoD) as low as 86 CFU/mL and 94 CFU/mL for S. typhimurium and S. enteritidis, respectively, that could be attributed to the high fluorescence collection efficiency of the SAF microlens array. These combinations reduced the duration of analysis to less than 3 h including sample preparation. This platform has the potential for wide application as a high-throughput biosensor to analyze pathogens in clinical, food, and environmental samples.

Rapid detection of foodborne pathogens at an early stage is imperative for preventing the outbreak of foodborne diseases, known as serious threats to human health. Conventional bacterial culturing methods for foodborne pathogen detection are time consuming, laborious, and with poor pathogen diagnosis competences. This has prompted researchers to call the current status of detection approaches into question and leverage new technologies for superior pathogen sensing outcomes. Novel strategies mainly rely on incorporating all the steps from sample preparation to detection in miniaturized devices for online monitoring of pathogens with high accuracy and sensitivity in a time-saving and cost effective manner. Lab on chip is a blooming area in diagnosis, which exploits different mechanical and biological techniques to detect very low concentrations of pathogens in food samples. This is achieved through streamlining the sample handling and concentrating procedures, which will subsequently reduce human errors and enhance the accuracy of the sensing methods. Integration of sample preparation techniques into these devices can effectively minimize the impact of complex food matrix on pathogen diagnosis and improve the limit of detections. Integration of pathogen capturing bio-receptors on microfluidic devices is a crucial step, which can facilitate recognition abilities in harsh chemical and physical conditions, offering a great commercial benefit to the food-manufacturing sector. This article reviews recent advances in current state-of-the-art of sample preparation and concentration from food matrices with focus on bacterial capturing methods and sensing technologies, along with their advantages and limitations when integrated into microfluidic devices for online rapid detection of pathogens in foods and food production line.

Background: Umbilical cord blood (UCB) is a rich source of hematopoietic stem cells and is useful for the treatment of blood diseases. The cost of UCB storage is high; thus, it is necessary to evaluate the quality of UCB before collection and cryopreservation. Aim: This study aimed to determine the maternal and neonatal factors that influence UCB before selection for cryopreservation. Materials and Methods: The analysis included 403 processed UCB units. The effects of maternal characteristics including maternal age and delivery method and neonatal factors such as birth weight, gestation duration, and sex on UCB quality were determined based on the collected blood volume, total nucleated cell (TNC) count, and CD34+ cell count. Results: The neonatal birth weight influenced the collected blood volume, TNC count, and CD34+ cell count. Neonates with higher birth weights produced better quality UCB units because of increased collected blood volumes, TNC counts, and CD34+ cell counts. However, an increase in the gestational age from 35 to 41 weeks led to decreases in the collected blood volume and CD34+ cell count. Conclusion: These data may be useful for determining the optimal cord blood units for collection and cryopreservation and for advising pregnant women using private banking services.

In this paper, we present, to the best of our knowledge, for the first time, in-depth theoretical analysis and experimental results for the optimisation of supercritical angle fluorescence (SAF) structures in polymer microfluidic chips fabricated from a combination of micro-milling and polymer injection-moulding techniques for their application in the highly-sensitive detection of pathogens. In particular, we address experimentally and theoretically the relationship between the supercritical angle and the heights of the SAF structures embedded in the microfluidic chips to obtain optimised results where the highest fluorescence intensity is collected, and hence determining the optimised limit of detection (LOD). Together with theoretical modelling, we experimentally fabricate microarrays of SAF structures with different heights varying from zero to the order of 300 μm in cyclic olefin copolymer (COC) microfluidic chips. The results show that for fluorophores at the interface of air and COC, the highest fluorescence intensities are obtained at SAF structures with a 163 μm height for a milling tool with a 97.4 μm diameter, which is in excellent agreement with our modelling. A fluorescence LOD of 5.42 × 104 molecules is achieved when using such SAF structures. The solid-phase polymerase chain reaction (SP-PCR) on these SAF structures permits sensitive pathogen detection (3.37 × 102 copies of the E. coli genome per μL) on-chip. These results especially are of interest for applications in hypersensitive pathogen detection as well as in assisting the design of devices for point-of-care applications. Findings on the height optimization of SAF structures also advance our understanding of SAF detection techniques and provide insights into the development of fluorescence microscopy.

Advanced free angle photolithography (FAPL) is presented for making 3D supercritical angle fluorescence (SAF) microstructures and transfer them on to polymeric chips using injection molding technique for low-cost microfluidic devices embedded with optical sensing structures. A solid phase polymerase chain reaction (SP-PCR) is used as model technique, which allows rapid and sensitive detection of pathogen DNA on-chip. This article presents the detailed fabrication of SAF structure and SP-PCR application on SAF structure for pathogen detection. This protocol of developing SAF structures using the FAPL process, increases the number of SAF per mm(2). FAPL was performed via a motorized stage to control the angle of incidence and to achieve the desired bucket-shapes (dimensions of 50 μm to 150 μm with a slope) required for the 3D optical sensing. Due to the unique properties of SAF structures, it enhances the fluorescent signal by 46 times. Increasing the number of SAF structures and reducing the size resulted in reduction of sample volume required per test along with improvement in the limit of detection (LOD) due to a smaller size. This article also presents the experimental details of SP-PCR using DNA oligos bound to the SAF structures for on-chip pathogen detection and a comparison between different sizes of SAF structures. The direct on-chip SP-PCR paves the path for the application of this technique in point-of-care devices.

Foodborne salmonellosis remains a major economic burden worldwide and particularly for food industries. The diverse and complexity of food matrices pose great challenges for rapid and ultra-sensitive detection of Salmonella in food samples. In this study, combination of pathogen pre-concentration with rapid molecular identification is presented to overcome these challenges. This combination enabled effective real-time PCR detection of low levels of Salmonella enterica serovar Typhimurium without culture enrichment. Anti-salmonella antibody, immobilized on protein AG-magnetic beads, could efficiently concentrate Salmonella Typhimurium with a capturing efficiency of 95%. In the direct PCR, a strong linear relationship between bacteria concentration and the number of cycles was observed with a relative PCR efficiency of ∼92% resulting in a limit of detection (LoD) of ∼2 CFU/mL. Analysis of spiked food samples that include vegetable salad, egg yolk, egg white, whole egg and minced pork meat has validated the precision of the method. A relative accuracy of 98.3% with a sensitivity of 91.6% and specificity of 100% was achieved in the Salmonella spiked food samples. The use of a Phusion hot start DNA polymerase with a high tolerance to possible PCR inhibitors allowed the integration of direct PCR, and thereby reducing the duration of analysis to less than 3 h. The Cohen's kappa index showed excellent agreement (0.88) signifying the capability of this method to overcome the food matrix effects in rapid and ultra-sensitive detection of Salmonella in food. This approach may lay a future platform for the integration into a Lab-on-a-chip system for online monitoring of foodborne pathogens.

Campylobacteriosis is one of the most common foodborne diseases worldwide. Two Campylobacter species – C. jejuni and C. coli in poultry and poultry products are considered to be the main source of human campylobacteriosis. Therefore, studying Campylobacter status in poultry flocks is needed to prevent transmission of disease and reduce human risk, health cost, and economic losses. In this study, we adapted and used a Loop-Mediated Isothermal Amplification (LAMP) assay for specific, sensitive, simple and cost-effective rapid detection of C. jejuni and C. coli in the poultry production chain. Amplified LAMP products were detected using a small, low-cost portable commercial blue LED transilluminator and a direct visual detection strategy was demonstrated. By using optimized conditions for amplification a limit of detection (LOD) of 50 CFU/ml was achieved for testing of C. jejuni and C. coli in spiked chicken feces without enrichment. The method took 60–70 min from receiving the samples to the final results (including 30 min for amplification). The optimized LAMP showed a relative accuracy of 98.4%, a specificity of 97.9%, and a sensitivity of 100% in comparison to real-time PCR method. Cohen’s kappa index also showed an excellent agreement (0.94) between the two methods. The results showed that the method is specific, sensitive and is suitable to develop for rapid detection of Campylobacter spp. at poultry production.

LAMP has received great interest and is widely utilized in life sciences for nucleic acid analysis. To monitor a real-time LAMP assay, a fluorescence DNA dye is an indispensable component and therefore the selection of a suitable dye for real-time LAMP is a need. To aid this selection, we investigated the inhibition effects of twenty-three DNA dyes on real-time LAMP. Threshold time (Tt) values of each real-time LAMP were determined and used as an indicator of the inhibition effect. Based on the inhibition effects, the dyes were classified into four groups: (1) non-inhibition effect, (2) medium inhibition effect, (3) high inhibition effect, and (4) very high inhibition effect. The signal to noise ratio (SNR) and the limit of detection (LOD) of the dyes in groups 1, 2, and 3 were further investigated, and possible inhibition mechanisms of the DNA dyes on the real-time LAMP are suggested and discussed. Furthermore, a comparison of SYTO 9 in different LAMP reactions and different systems is presented. Of the 23 dyes tested, SYTO 9, SYTO 82, SYTO 16, SYTO 13, and Miami Yellow were the best dyes with no inhibitory effect, low LOD and high SNR in the real-time LAMP reactions. The present classification of the dyes will simplify the selection of fluorescence dye for real-time LAMP assays in point of care setting.

Three novel hydrogen-generating strains, ST1, ST4, and ST5, were isolated from the rumen of cow in Vietnam, and respectively identified as Clostridium beijerinckii ST1, Clostridium bifermentans ST4, and Clostridium butyricum ST5, based on 16S rDNA gene sequence analysis and physiobiochemical characteristics. The dark fermentative hydrogen production of these isolated Clostridium strains was performed and characterized in both pure- and co-cultures from various carbon sources including sucrose, glucose, lactose, xylose, molasses, cassava stumps, and rice distillers wet grains with soluble. The highest hydrogen production was achieved from a co-culture with three Clostridium strains. To optimize the operational conditions of temperature, time, and substrate concentration for the high-level production of hydrogen, response surface methodology in a Box-Behnken design was used. The results revealed a maximum hydrogen production of 1.13 ± 0.015 L H2/L medium by the three-strain co-culture under the following fermentation conditions: 11.63 g/L sucrose, 36.1 °C, in 51.13 h.

A modular adaptor consisting of a sequence-specific DNA binding zinc finger protein and a self-ligating protein-tag was developed to expedite efficient formation of a covalent linkage between an individual protein molecule and the programmed address modified with a tag-substrate on the DNA nanostructure.

We report the construction of an artificial enzyme cascade based on the xylose metabolic pathway. Two enzymes, xylose reductase and xylitol dehydrogenase, were assembled at specific locations on DNA origami by using DNA-binding protein adaptors with systematic variations in the interenzyme distances and defined numbers of enzyme molecules. The reaction system, which localized the two enzymes in close proximity to facilitate transport of reaction intermediates, resulted in significantly higher yields of the conversion of xylose into xylulose through the intermediate xylitol with recycling of the cofactor NADH. Analysis of the initial reaction rate, regenerated amount of NADH, and simulation of the intermediates' diffusion indicated that the intermediates diffused to the second enzyme by Brownian motion. The efficiency of the cascade reaction with the bimolecular transport of xylitol and NAD(+) likely depends more on the interenzyme distance than that of the cascade reaction with unimolecular transport between two enzymes.

Biohydrogen production from xylose by Thermotoga neapolitana was investigated in batch culture using serum bottles and a continuously stirred anaerobic bioreactor (CSABR). The effect of various xylose concentrations on growth and H2 production were studied in small batch culture for highly efficient H2 production. The highest hydrogen production of 32.1 ± 1.6 mmol-H2/L and maximum biomass concentration of 959.63 ± 47.9 mg/L were obtained at initial xylose concentration of 5.0 g/L. To develop a large-scale biohydrogen production system as well as overcome the problems in small batch culture, a continuously stirred anaerobic bioreactor was tested on T. neapolitana in both pH-uncontrolled batch culture and pH-controlled batch culture. The results showed that the production level of H2 from fermentation in a pH-controlled batch culture was much higher than those from a pH-uncontrolled batch culture for H2 production from xylose. The H2 yield in a pH-controlled batch culture on xylose substrate was 2.22 ± 0.11 mol-H2 mol−1 xyloseconsumed, which was nearly 1.2-fold higher than pH-uncontrolled batch cultures. In order to study the precise effect of a stable pH on hydrogen production, and metabolite pathway involved, cultures was conducted with pH-controlled at different levels ranging from 6.5 to 7.5. The maximum H2 yield of 2.8 ± 0.14 mol-H2 mol−1 xyloseconsumed was measured while the pH was maintained at 7.0. The acetic acid and lactic acid production were 2.98 ± 0.15 g/L and 0.36 ± 0.02 g/L, respectively.

Biohydrogen fermentation by the hyperthermophile Thermotoga neapolitana was conducted in a continuously stirred anaerobic bioreactor (CSABR). The production level of H 2 from fermentation in a batch culture with pH control was much higher than without pH control from pentose (xylose) and hexose (glucose and sucrose) substrates. The respective H 2 yield in the batch culture with pH control from xylose and glucose was 2.22 ± 0.11 mol-H 2 mol −1 xylose consumed and 3.2 ± 0.16 mol-H 2 mol −1 glucose consumed , which was nearly 1.2-fold greater for xylose and 1.6-fold greater for glucose than without pH control. In the case of sucrose, the H 2 yield from fermentation increased by 40.63%, compared with fermentation in batch cultures without pH control, from 3.52 ± 0.171 to 4.95 ± 0.25 mol-H 2 mol −1 sucrose consumed . The effects of stirring speed and different pH levels on growth and H 2 production were studied in the CSABR for highly efficient H 2 production. Growth and H 2 production of this bacterial strain in a batch culture with pH control or without pH control using a 3 L bioreactor was limited within 24 h due to substrate exhaustion and a decrease in the culture’s pH. The pH-controlled fed-batch culture with a xylose substrate added in doses was studied for the prevention of substrate-associated growth inhibition by controlling the nutrient supply. The highest H 2 production rates were approximately 4.6, 4.1, 3.9, and 4.3 mmol-H 2 L −1 h −1 at 32, 52, 67, and 86 h, respectively.

Efficient conversion of glycerol waste from biodiesel manufacturing processes into biohydrogen by the hyperthermophilic eubacterium Thermotoga neapolitana DSM 4359 was investigated. Biohydrogen production by T. neapolitana was examined using the batch cultivation mode in culture medium containing pure glycerol or glycerol waste as the sole substrate. Pre-treated glycerol waste showed higher hydrogen (H2) production than untreated waste. Nitrogen (N2) sparging and pH control were successfully implemented to maintain the culture pH and to reduce H2 partial pressure in the headspace for optimal growth rate and to enhance hydrogen production from the glycerol waste. It was found that hydrogen production increased from 1.24 ± 0.06 to 1.98 ± 0.1 mol-H2 mol−1 glycerolconsumed by optimising N2 sparging and pH control. We observed that in medium containing 0.05 M HEPES, with three cycles of N2 sparging, the H2 yield increased to 2.73 ± 0.14 mol-H2 mol−1 glycerolconsumed, which was 2.22-fold higher than the non-N2 sparged H2 yield (1.23 ± 0.06 mol-H2 mol−1 glycerolconsumed).

The addressable DNA nanostructures offer ideal platforms to construct organized assemblies of multiple protein molecules. Sequence-specific DNA binding proteins that target defined sites on DNA nanostructures would act as orthogonal adaptors to carry individual protein molecules to the programmed addresses. We have recently developed a protein-based adaptor by utilizing the sequence-specific DNA binding zinc finger protein to locate a monomeric protein of interest at specific positions on DNA origami, which serves as a molecular switchboard. We herein report a new adaptor to locate a protein dimer on the DNA origami scaffold based on a homodimeric basic-leucine zipper protein GCN4. Specific binding of GCN4 to programmed addresses on DNA origami and orthogonal targeting by GCN4- and zinc finger protein-based adaptors to the respective addresses on DNA origami were confirmed by gel electrophoretic and AFM analyses. Furthermore, a GCN4-fused homodimeric enzyme showed even higher activity than the wild type enzyme, and exhibited avid reactivity when assembled at the specific site of DNA origami. Thus, GCN4 serves as an ideal adaptor to locate homodimeric proteins in the functional form on DNA origami.

Biohydrogen fermentation using immobilized cells of Thermotoga neapolitana on porous glass beads was successfully performed in a continuously stirring anaerobic bioreactor (CSABR) system operated under the conditions of temperature 75 o C, pH 7.0 and 5.0 g/L pentose (xylose) and/or hexose (glucose). The results showed that both batch and fed-batch cultivations of the immobilized cells were effective for high-rate and high-yield H 2 production compared with those from the free cells. In the batch cultivation, the H 2 production rate and H 2 production yield of the immobilized cells, respectively achieved the highest values of 5.64 ± 0.19 mmol-H 2 L -1 h -1 and 1.84 ± 0.1 mol H 2 /mol xylose, which were almost 1.7-fold and 1.3-fold higher than those with free cells. The maximum H 2 production rate ­ (6.91 mmol L -1 h -1 ) in this proposed method was 1.5-fold higher than that of free cells in the fed-batch cultivation.

The volume of point of care (POC) testing continues to grow steadily due to the increased availability of easy-to-use devices, thus making it possible to deliver less costly care closer to the patient site in a shorter time relative to the central laboratory services. A novel class of molecules called microRNAs have recently gained attention in healthcare management for their potential as biomarkers for human diseases. The increasing interest of miRNAs in clinical practice has led to an unmet need for assays that can rapidly and accurately measure miRNAs at the POC. However, the most widely used methods for analyzing miRNAs, including Northern blot-based platforms, in situ hybridization, reverse transcription qPCR, microarray, and next-generation sequencing, are still far from being used as ideal POC diagnostic tools, due to considerable time, expertize required for sample preparation, and in terms of miniaturizations making them suitable platforms for centralized labs. In this review, we highlight various existing and upcoming technologies for miRNA amplification and detection with a particular emphasis on the POC testing industries. The review summarizes different miRNA targets and signals amplification-based assays, from conventional methods to alternative technologies, such as isothermal amplification, paper-based, oligonucleotide-templated reaction, nanobead-based, electrochemical signaling-based, and microfluidic chip-based strategies. Based on critical analysis of these technologies, the possibilities and feasibilities for further development of POC testing for miRNA diagnostics are addressed and discussed. The RightsLink Digital Licensing and Rights Management Service (including RightsLink for Open Access) is available (A) to users of copyrighted works found at the websites of participating publishers who are seeking permissions or licenses to use those works, and (B) to authors of articles and other manuscripts who are seeking to pay author publication charges in connection with the submission of their works to publishers. SMARTDIAGNOS